The Trump administration deported a 31-year-old Salvadoran man minutes after a federal appeals court barred his removal while his case proceeded, the government admitted in a court filing this week.

In its filing, the government denied that it had violated the order from the U.S. Court of Appeals for the Second Circuit, in New York, instead blaming “a confluence of administrative errors.” The filing argues that because the process of deporting the man, Jordin Melgar-Salmeron, had already started before the court issued its formal order, at 9:52 a.m. May 7, that meant the order had not been violated.

The plane carrying Mr. Melgar-Salmeron to El Salvador did not take off from Alexandria, La., until 10:20 a.m. Eastern time, according to the government’s timeline. The government had also previously given the court what the judges called “express assurance” that it would not schedule a deportation for him until the next day.

The deportation deepened the questions surrounding the Trump administration’s legal tactics and administrative errors as it has sought to carry out the president’s aggressive vision of deporting as many as one million immigrants during his first year in office. In at least three other deportation cases, federal judges have determined that Trump officials expelled people from the country in violation of standing court orders.

In an interview, one of Mr. Melgar-Salmeron’s lawyers disputed the government’s characterization of the deportation as a mistake, saying it appeared to be part of a larger pattern of the administration ignoring court orders. “It would be an absurd level of mistake,” said Matthew Borowski, the lawyer, comparing it to a chef pouring in pepper instead of salt. “Verifying the paperwork and putting the right people on the plane is their job.”

The questions raised by the court over the deportation were reported earlier by Investigative Post, a nonprofit news outlet in Western New York.